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Integration of single-cell multi-omic data with graph-based topic modelling

Malagoli, G.; Valle, F.; Tirabassi, A.; Marsico, A.; Martignetti, L.; Caselle, M.; Colome-Tatche, M.

2026-02-26 bioinformatics
10.64898/2026.02.25.707947 bioRxiv
Show abstract

Recent advances in single-cell biology enable the profiling of multiple molecular layers, such as the transcriptome, epigenome, and surface proteins, within a single cell. Tackling the complexity of these data from different perspectives allows researchers to get the most complete insights into the biological properties of cells. Here, we propose a graph-based topic modelling method called bionSBM. Our method leverages well-known community-detection methods for multipartite graphs and the interpretability of topic modelling to cluster and explain high-dimensional, sparse, and noisy single-cell matrices. We applied our algorithm to paired single-cell multi-omics data, such as 10X Multiome, SHARE-seq, and CITE-seq. We showed that it achieves superior performance compared to state-of-the-art methods for ground-truth label retrieval, with high specificity and distinct biological interpretability.

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